PROSITE documentation PDOC51710OBG-type guanine nucleotide-binding (G) domain profile
The P-loop (see <PDOC00017>) guanosine triphosphatases (GTPases) control a multitude of biological processes, ranging from cell division, cell cycling, and signal transduction, to ribosome assembly and protein synthesis. GTPases exert their control by interchanging between an inactive GDP-bound state and an active GTP-bound state, thereby acting as molecular switches. The common denominator of GTPases is the highly conserved guanine nucleotide-binding (G) domain that is responsible for binding and hydrolysis of guanine nucleotides.
Within the translation factor-related (TRAFAC) class of P-loop GTPases, the OBG family comprises a group of high-molecular mass GTPases conserved from bacteria to eukaryotes. The OBG family consists of [1]:
- Obg from bacteria and eukaryotes [2,3].
- DRG from eukaryotes and archaea. DRG proteins may regulate fundamental cellular processes through RNA binding [4].
- Nog1 from eukaryotes and archaea. It is involved in the assembly of the large ribosomal subunit.
- Yyaf/YchF from bacteria and eukaryotes. It consists of a central G domain, flanked by a coiled-coil domain and a TGS (ThrRS, GTPase, SpoT) domain (see <PDOC51880>). Members of this subfamily bind and hydolyze ATP more efficiently than GTP [5,6].
- Ygr210 from archaea and fungi.
The OBG-type G domain has a mononucleotide binding fold typical for the P-loop NTPases. A six-stranded mostly parallel β-sheet is flanked by α-helices on both sides (see <PDB:1JAL>). The OBG-type G domain contains five characteristic sequence motifs, termed G1-G5, involved in nucleotide binding and hydrolysis. The G1/Walker A motif (GXXXXGK(S/T)), also referred to as P-loop, helps to position the triphosphate moiety of the bound nucleotide. The G2 (X(T/S)X) and G3/Walker B (hhhDXXG) motifs are involved in the coordination of a Mg(2)+ ion that is required for nucleotide binding and hydrolysis. Specificity in nucleotide binding is conferred by the G4 motif, which has a (N/T)KXD signature in guanine nucleotide binding P-loop NTPases. The G5 motif ((T/G)(C/S)A) supports guanine base recognition [2,3,5,6].
The profile we developed covers the entire OBG-type G domain.
Last update:March 2014 / First entry.
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PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | Leipe D.D. Wolf Y.I. Koonin E.V. Aravind L. |
| Title | Classification and evolution of P-loop GTPases and related ATPases. | |
| Source | J. Mol. Biol. 317:41-72(2002). | |
| PubMed ID | 11916378 | |
| DOI | 10.1006/jmbi.2001.5378 |
| 2 | Authors | Buglino J. Shen V. Hakimian P. Lima C.D. |
| Title | Structural and biochemical analysis of the Obg GTP binding protein. | |
| Source | Structure 10:1581-1592(2002). | |
| PubMed ID | 12429099 |
| 3 | Authors | Kukimoto-Niino M. Murayama K. Inoue M. Terada T. Tame J.R.H. Kuramitsu S. Shirouzu M. Yokoyama S. |
| Title | Crystal structure of the GTP-binding protein Obg from Thermus thermophilus HB8. | |
| Source | J. Mol. Biol. 337:761-770(2004). | |
| PubMed ID | 15019792 | |
| DOI | 10.1016/j.jmb.2004.01.047 |
| 4 | Authors | Ishikawa K. Azuma S. Ikawa S. Morishita Y. Gohda J. Akiyama T. Semba K. Inoue J.i. |
| Title | Cloning and characterization of Xenopus laevis drg2, a member of the developmentally regulated GTP-binding protein subfamily. | |
| Source | Gene 322:105-112(2003). | |
| PubMed ID | 14644502 |
| 5 | Authors | Teplyakov A. Obmolova G. Chu S.Y. Toedt J. Eisenstein E. Howard A.J. Gilliland G.L. |
| Title | Crystal structure of the YchF protein reveals binding sites for GTP and nucleic acid. | |
| Source | J. Bacteriol. 185:4031-4037(2003). | |
| PubMed ID | 12837776 |
| 6 | Authors | Koller-Eichhorn R. Marquardt T. Gail R. Wittinghofer A. Kostrewa D. Kutay U. Kambach C. |
| Title | Human OLA1 defines an ATPase subfamily in the Obg family of GTP-binding proteins. | |
| Source | J. Biol. Chem. 282:19928-19937(2007). | |
| PubMed ID | 17430889 | |
| DOI | 10.1074/jbc.M700541200 |
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